external_reference/README.md

External Reference Data

This folder is the clean, reusable external-data surface for Z-Screen benchmarking.

Start with:

• catalog/processing_provenance.md for what was copied, converted, and not recomputed.
• catalog/external_reference_dataset_catalog.csv for dataset-level entry points.
• catalog/external_reference_file_manifest.csv for file-level hashes and legacy source aliases.

Most experiments should use the Parquet tables under:

• crispr_perturbation_atlases/ for Replogle, Norman, and selected THP1 scPerturb CRISPR comparisons.
• compound_atlases/lincs_l1000/processed/ for LINCS L1000 compound signature comparisons.
• compound_atlases/tahoe_100m/metadata/ for Tahoe metadata-only overlap checks.

benchmark_outputs/ contains the prior LINCS versus Z-Screen overlap/correlation outputs from the legacy benchmark bundle. Treat those as historical benchmark outputs, not as primary external atlas inputs.

Raw external H5AD and LINCS GCTX matrices are not bundled here. The processed rank-signature tables and provenance scripts are bundled so downstream experiments do not need to rebuild them for routine comparisons.